diff --git a/episodes/figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png b/episodes/figures/curatedAtlasQuery.png similarity index 100% rename from episodes/figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png rename to episodes/figures/curatedAtlasQuery.png diff --git a/episodes/hca.Rmd b/episodes/hca.Rmd index 6be8def..65473e5 100644 --- a/episodes/hca.Rmd +++ b/episodes/hca.Rmd @@ -69,7 +69,7 @@ bulk counts are also available to facilitate large-scale, summary analyses of transcriptional profiles. This platform offers a standardized workflow for accessing atlas-level datasets programmatically and reproducibly. -![](figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png) +![](figures/curatedAtlasQuery.png) # Data Sources in R / Bioconductor diff --git a/episodes/intro-sce.Rmd b/episodes/intro-sce.Rmd index baa3995..1e66c37 100644 --- a/episodes/intro-sce.Rmd +++ b/episodes/intro-sce.Rmd @@ -23,9 +23,9 @@ exercises: 10 # Minutes of exercises in the lesson # Setup ```{r setup, message = FALSE, warning=FALSE} -library("SummarizedExperiment") -library("SingleCellExperiment") -library("MouseGastrulationData") +library(SummarizedExperiment) +library(SingleCellExperiment) +library(MouseGastrulationData) library(BiocStyle) ``` diff --git a/episodes/large_data.Rmd b/episodes/large_data.Rmd index 92b42a1..8311c02 100644 --- a/episodes/large_data.Rmd +++ b/episodes/large_data.Rmd @@ -17,7 +17,7 @@ exercises: 2 # Minutes of exercises in the lesson - Learn how to work with out-of-memory data representations such as HDF5. - Learn how to speed up single-cell analysis with parallel computation. - Learn how to invoke fast approximations for essential analysis steps. -- Learn how to convert SingleCellExperiment objects to SeuratObjects and AnnData objects. +- Learn how to convert `SingleCellExperiment` objects to `SeuratObject`s and `AnnData` objects. :::::::::::::::::::::::::::::::::::::::::::::::: @@ -526,7 +526,7 @@ Use Seurat's `DimPlot` function. ::::::::::::::::::::::::::::::::::::: keypoints -- Out-of-memory representations can be used to work with single-cell datasets that are too large to fit in memory +- Out-of-memory representations can be used to work with single-cell datasets that are too large to fit in memory - Parallelization of calculations across genes or cells is an effective strategy for speeding up analysis of large single-cell datasets - Fast approximations for nearest neighbor search and singular value composition can speed up essential steps of single-cell analysis with minimal loss of accuracy - Converter functions between existing single-cell data formats enable analysis workflows that leverage complementary functionality from poplular single-cell analysis ecosystems